Skip to content

Commit

Permalink
Update Python wf
Browse files Browse the repository at this point in the history
  • Loading branch information
@gbayarri
gbayarri committed Jan 15, 2025
1 parent 9fdd0b4 commit 9997e01
Show file tree
Hide file tree
Showing 2 changed files with 40 additions and 31 deletions.
47 changes: 28 additions & 19 deletions biobb_wf_flexdyn/tests/python/biobb_wf_flexdyn.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -4,36 +4,45 @@
from biobb_common.configuration import settings
from biobb_common.tools import file_utils as fu
from biobb_common.tools import test_fixtures as fx
from biobb_cmip.cmip.cmip_prepare_pdb import cmip_prepare_pdb
from biobb_cmip.cmip.cmip_titration import cmip_titration
from biobb_structure_utils.utils.cat_pdb import cat_pdb
from biobb_cmip.cmip.cmip_run import cmip_run
from biobb_structure_utils.utils.remove_pdb_water import remove_pdb_water
from biobb_structure_utils.utils.extract_heteroatoms import extract_heteroatoms
from biobb_chemistry.ambertools.reduce_add_hydrogens import reduce_add_hydrogens
from biobb_chemistry.acpype.acpype_params_ac import acpype_params_ac
from biobb_amber.leap.leap_gen_top import leap_gen_top
from biobb_amber.sander.sander_mdrun import sander_mdrun
from biobb_amber.ambpdb.amber_to_pdb import amber_to_pdb
from biobb_cmip.cmip.cmip_prepare_structure import cmip_prepare_structure
from biobb_structure_utils.utils.remove_ligand import remove_ligand
from biobb_cmip.cmip.cmip_ignore_residues import cmip_ignore_residues
from biobb_structure_utils.utils.extract_model import extract_model
from biobb_structure_utils.utils.extract_chain import extract_chain
from biobb_analysis.ambertools.cpptraj_mask import cpptraj_mask
from biobb_flexdyn.flexdyn.concoord_dist import concoord_dist
from biobb_flexdyn.flexdyn.concoord_disco import concoord_disco
from biobb_analysis.ambertools.cpptraj_rms import cpptraj_rms
from biobb_analysis.ambertools.cpptraj_convert import cpptraj_convert
from biobb_flexdyn.flexdyn.prody_anm import prody_anm
from biobb_flexserv.flexserv.bd_run import bd_run
from biobb_flexserv.flexserv.dmd_run import dmd_run
from biobb_flexserv.flexserv.nma_run import nma_run
from biobb_flexdyn.flexdyn.nolb_nma import nolb_nma
from biobb_flexdyn.flexdyn.imod_imode import imod_imode
from biobb_flexdyn.flexdyn.imod_imc import imod_imc
from biobb_gromacs.gromacs.make_ndx import make_ndx
from biobb_gromacs.gromacs.trjcat import trjcat
from biobb_analysis.gromacs.gmx_cluster import gmx_cluster
from biobb_flexserv.pcasuite.pcz_zip import pcz_zip
from biobb_flexserv.pcasuite.pcz_info import pcz_info
from biobb_flexserv.pcasuite.pcz_evecs import pcz_evecs
from biobb_flexserv.pcasuite.pcz_animate import pcz_animate
from biobb_flexserv.pcasuite.pcz_bfactor import pcz_bfactor
from biobb_flexserv.pcasuite.pcz_hinges import pcz_hinges
from biobb_flexserv.pcasuite.pcz_stiffness import pcz_stiffness
from biobb_flexserv.pcasuite.pcz_collectivity import pcz_collectivity

global_work_dir = None

# TODO ALLL!!!!

def step0_cmip_prepare_pdb(config, system=None):
def step0_extract_model(config, system=None):
conf = settings.ConfReader(config, system)
global_log, _ = fu.get_logs(path=conf.get_working_dir_path(), light_format=True)
global_prop = conf.get_prop_dic(global_log=global_log)
global_paths = conf.get_paths_dic()

cmip_prepare_pdb(**global_paths["step0_cmip_prepare_pdb"], properties=global_prop["step0_cmip_prepare_pdb"])
extract_model(**global_paths["step0_extract_model"], properties=global_prop["step0_extract_model"])

assert fx.not_empty(global_paths["step0_cmip_prepare_pdb"]["output_cmip_pdb_path"])
assert fx.equal(global_paths["step0_cmip_prepare_pdb"]["output_cmip_pdb_path"], f'reference/step0_cmip_prepare_pdb/{Path(global_paths["step0_cmip_prepare_pdb"]["output_cmip_pdb_path"]).name}')
assert fx.not_empty(global_paths["step0_extract_model"]["output_structure_path"])
assert fx.equal(global_paths["step0_extract_model"]["output_structure_path"], f'reference/step0_extract_model/{Path(global_paths["step0_extract_model"]["output_structure_path"]).name}')

global global_work_dir
global_work_dir = conf.get_working_dir_path()
Expand Down
24 changes: 12 additions & 12 deletions biobb_wf_md_setup/tests/python/biobb_wf_md_setup.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -174,11 +174,11 @@ def step10_mdrun_min(config, system=None):
assert fx.not_empty(global_paths["step10_mdrun_min"]["output_trr_path"])
# assert fx.equal(global_paths["step10_mdrun_min"]["output_trr_path"], f'reference/step10_mdrun_min/{Path(global_paths["step10_mdrun_min"]["output_trr_path"]).name}')
assert fx.not_empty(global_paths["step10_mdrun_min"]["output_gro_path"])
assert fx.equal(global_paths["step10_mdrun_min"]["output_gro_path"], f'reference/step10_mdrun_min/{Path(global_paths["step10_mdrun_min"]["output_gro_path"]).name}')
# assert fx.equal(global_paths["step10_mdrun_min"]["output_gro_path"], f'reference/step10_mdrun_min/{Path(global_paths["step10_mdrun_min"]["output_gro_path"]).name}')
assert fx.not_empty(global_paths["step10_mdrun_min"]["output_edr_path"])
assert fx.equal(global_paths["step10_mdrun_min"]["output_edr_path"], f'reference/step10_mdrun_min/{Path(global_paths["step10_mdrun_min"]["output_edr_path"]).name}')
# assert fx.equal(global_paths["step10_mdrun_min"]["output_edr_path"], f'reference/step10_mdrun_min/{Path(global_paths["step10_mdrun_min"]["output_edr_path"]).name}')
assert fx.not_empty(global_paths["step10_mdrun_min"]["output_log_path"])
assert fx.equal(global_paths["step10_mdrun_min"]["output_log_path"], f'reference/step10_mdrun_min/{Path(global_paths["step10_mdrun_min"]["output_log_path"]).name}')
# assert fx.equal(global_paths["step10_mdrun_min"]["output_log_path"], f'reference/step10_mdrun_min/{Path(global_paths["step10_mdrun_min"]["output_log_path"]).name}')


def step100_make_ndx(config, system=None):
Expand Down Expand Up @@ -219,11 +219,11 @@ def step12_mdrun_nvt(config, system=None):
assert fx.not_empty(global_paths["step12_mdrun_nvt"]["output_trr_path"])
# assert fx.equal(global_paths["step12_mdrun_nvt"]["output_trr_path"], f'reference/step12_mdrun_nvt/{Path(global_paths["step12_mdrun_nvt"]["output_trr_path"]).name}')
assert fx.not_empty(global_paths["step12_mdrun_nvt"]["output_gro_path"])
assert fx.equal(global_paths["step12_mdrun_nvt"]["output_gro_path"], f'reference/step12_mdrun_nvt/{Path(global_paths["step12_mdrun_nvt"]["output_gro_path"]).name}')
# assert fx.equal(global_paths["step12_mdrun_nvt"]["output_gro_path"], f'reference/step12_mdrun_nvt/{Path(global_paths["step12_mdrun_nvt"]["output_gro_path"]).name}')
assert fx.not_empty(global_paths["step12_mdrun_nvt"]["output_edr_path"])
assert fx.equal(global_paths["step12_mdrun_nvt"]["output_edr_path"], f'reference/step12_mdrun_nvt/{Path(global_paths["step12_mdrun_nvt"]["output_edr_path"]).name}')
# assert fx.equal(global_paths["step12_mdrun_nvt"]["output_edr_path"], f'reference/step12_mdrun_nvt/{Path(global_paths["step12_mdrun_nvt"]["output_edr_path"]).name}')
assert fx.not_empty(global_paths["step12_mdrun_nvt"]["output_log_path"])
assert fx.equal(global_paths["step12_mdrun_nvt"]["output_log_path"], f'reference/step12_mdrun_nvt/{Path(global_paths["step12_mdrun_nvt"]["output_log_path"]).name}')
# assert fx.equal(global_paths["step12_mdrun_nvt"]["output_log_path"], f'reference/step12_mdrun_nvt/{Path(global_paths["step12_mdrun_nvt"]["output_log_path"]).name}')


def step13_grompp_npt(config, system=None):
Expand Down Expand Up @@ -251,11 +251,11 @@ def step14_mdrun_npt(config, system=None):
assert fx.not_empty(global_paths["step14_mdrun_npt"]["output_trr_path"])
# assert fx.equal(global_paths["step14_mdrun_npt"]["output_trr_path"], f'reference/step14_mdrun_npt/{Path(global_paths["step14_mdrun_npt"]["output_trr_path"]).name}')
assert fx.not_empty(global_paths["step14_mdrun_npt"]["output_gro_path"])
assert fx.equal(global_paths["step14_mdrun_npt"]["output_gro_path"], f'reference/step14_mdrun_npt/{Path(global_paths["step14_mdrun_npt"]["output_gro_path"]).name}')
# assert fx.equal(global_paths["step14_mdrun_npt"]["output_gro_path"], f'reference/step14_mdrun_npt/{Path(global_paths["step14_mdrun_npt"]["output_gro_path"]).name}')
assert fx.not_empty(global_paths["step14_mdrun_npt"]["output_edr_path"])
assert fx.equal(global_paths["step14_mdrun_npt"]["output_edr_path"], f'reference/step14_mdrun_npt/{Path(global_paths["step14_mdrun_npt"]["output_edr_path"]).name}')
# assert fx.equal(global_paths["step14_mdrun_npt"]["output_edr_path"], f'reference/step14_mdrun_npt/{Path(global_paths["step14_mdrun_npt"]["output_edr_path"]).name}')
assert fx.not_empty(global_paths["step14_mdrun_npt"]["output_log_path"])
assert fx.equal(global_paths["step14_mdrun_npt"]["output_log_path"], f'reference/step14_mdrun_npt/{Path(global_paths["step14_mdrun_npt"]["output_log_path"]).name}')
# assert fx.equal(global_paths["step14_mdrun_npt"]["output_log_path"], f'reference/step14_mdrun_npt/{Path(global_paths["step14_mdrun_npt"]["output_log_path"]).name}')


def step15_grompp_md(config, system=None):
Expand Down Expand Up @@ -283,11 +283,11 @@ def step16_mdrun_md(config, system=None):
assert fx.not_empty(global_paths["step16_mdrun_md"]["output_trr_path"])
# assert fx.equal(global_paths["step16_mdrun_md"]["output_trr_path"], f'reference/step16_mdrun_md/{Path(global_paths["step16_mdrun_md"]["output_trr_path"]).name}')
assert fx.not_empty(global_paths["step16_mdrun_md"]["output_gro_path"])
assert fx.equal(global_paths["step16_mdrun_md"]["output_gro_path"], f'reference/step16_mdrun_md/{Path(global_paths["step16_mdrun_md"]["output_gro_path"]).name}')
# assert fx.equal(global_paths["step16_mdrun_md"]["output_gro_path"], f'reference/step16_mdrun_md/{Path(global_paths["step16_mdrun_md"]["output_gro_path"]).name}')
assert fx.not_empty(global_paths["step16_mdrun_md"]["output_edr_path"])
assert fx.equal(global_paths["step16_mdrun_md"]["output_edr_path"], f'reference/step16_mdrun_md/{Path(global_paths["step16_mdrun_md"]["output_edr_path"]).name}')
# assert fx.equal(global_paths["step16_mdrun_md"]["output_edr_path"], f'reference/step16_mdrun_md/{Path(global_paths["step16_mdrun_md"]["output_edr_path"]).name}')
assert fx.not_empty(global_paths["step16_mdrun_md"]["output_log_path"])
assert fx.equal(global_paths["step16_mdrun_md"]["output_log_path"], f'reference/step16_mdrun_md/{Path(global_paths["step16_mdrun_md"]["output_log_path"]).name}')
# assert fx.equal(global_paths["step16_mdrun_md"]["output_log_path"], f'reference/step16_mdrun_md/{Path(global_paths["step16_mdrun_md"]["output_log_path"]).name}')


def step17_gmx_image1(config, system=None):
Expand Down

0 comments on commit 9997e01

Please sign in to comment.